Students who take one of the government's flagship new diplomas could find themselves barred from the country's leading universities after research revealed admissions officers in some elite institutions are sceptical about the academic credentials of the new qualification.

Hundreds of pupils will be awarded the first diplomas on Thursday along with this year's GCSE results but the government-commissioned study, published today, suggested that some admissions officers regard them as more appropriate for students applying to ex-polytechnics than the top institutions.

The vast majority of universities surveyed welcomed the design of the qualifications – which allows students to specialise and do a dissertation-style extended essay – but many suggested that their success depended on the quality of teaching pupils receive.

Ed Balls, the schools secretary, has said he wants the diplomas to be the "qualification of choice" over A-levels and GCSEs. They are designed to bridge the gap between academic study and vocational training to give pupils broader skills once they leave school. If the leading universities reject diploma students it would be a serious blow to the scheme, undermining its academic reputation.

Today's study, by academics at the University of Exeter and commissioned by the Department for Children, Schools and Families, found that admissions officers in the most competitive universities are more likely to question the "academic rigour of diploma content" than at other institutions.

It found that nearly all universities will accept candidates from at least one of the current five diploma subjects, but all are expecting students to do at least one A-level as well to qualify for a place. Admissions officers will publish details of which combinations of diploma and A-levels they will accept but the report acknowledges that the information will come too late for the students awarded diplomas this summer.

The survey of senior manages and admissions tutors at 19 unnamed universities – representing the spread of different institutions in the UK – found that admissions tutors in new universities were more likely than those in elite institutions (69% compared to 57%) to accept the diploma as equivalent to 3.5 A-levels – the scoring recommended by the admissions authority, Ucas.

The report said: "None of the managers in 'research-intensive' HEIs [higher education institutions] reported high levels of internal support for diplomas at this stage. Phrases used were: 'degrees of scepticism', 'cautious', 'a way to go', 'quite cynical'. In contrast, half of the HEIs characterised by a predominantly teaching 'mission' used different phrases: 'a great deal of support across the board', 'support is strong', 'seen as legitimate', some departments are 'very positive'. The remainder reported a generally cautious stance among staff at this stage."

Two-thirds of those surveyed in top universities and one other from a "mid-ranking" institution said – unprompted – that they considered diplomas "more relevant to post-1992 universities". Respondents at two of the newer universities thought diplomas might well be ignored by elite institutions, creating a bigger divide between different institutions.

Those surveyed in the research-intensive universities were "more likely to examine closely the academic rigour of diploma content" and "less likely to assume that diploma study would turn out to have been adequate preparation for HE [higher education] entry," the report says.

The first few years would be crucial to establishing the diploma's reputation, it argues, and institutions will closely monitor the quality of candidates arriving at university from diploma courses and their drop-out rates.

A spokesman for the Conservatives said: "It would be a tragedy if young people who have been encouraged by the government to take the new diplomas then find that they become a block on opportunity. We want the new vocational diplomas to work so that there is a high-quality alternative. But if Ed Balls does not get these reforms right, a whole generation of children will be let down, with the poorest likely to suffer most."

The government strongly defended the diploma, insisting the overall message of the report is positive. Schools minister, Diana Johnson, said: "The report found that universities from all four mission groups, including the Russell Group and the 94 Group, have said they will accept diploma students on to a very wide range of courses.

"As always, the top selective universities tend to be more demanding in their entry criteria, whether they are considering A-level or diploma candidates ... It is important to remember that the surveys for this report were carried out in 2008 ... The more universities see of diplomas and diploma candidates, the more they welcome the knowledge, skills and experience they can bring to undergraduate study."

What is a diploma?

The diplomas are Labour's most radical reforms to the qualifications system. Designed to bridge the academic and vocational divide in schools, they allow students to study a specialist area in depth, while maintaining breadth by learning English and maths, as well as doing work experience and an extended essay.

Who is taking them?

Teaching started last September with 12,000 students taking one of the first five subjects – construction, IT, media, engineering and society, health and development.

Pupils from 14-19 take them at three levels: foundation (equivalent to a D-G grade at GCSE), higher (equivalent to A* to C at GCSE) and advanced (equivalent to A-level).

By 2011 every pupil should be able to opt for one of 12 diplomas. Colleges and schools have to form consortiums to offer the full range of diplomas, A-levels and GCSEs.

Will they work?

There have been widely documented concerns about their implementation after the government downscaled its ambitions this year from 50,000 students to just 12,000. But Ed Balls has announced a further three academic diplomas – in science, languages and humanities. He wants diplomas to become the "qualification of choice" over GCSE and A-levels. The Conservatives say if they win the next general election they will scrap the academic lines, to focus on diplomas becoming high-quality vocational qualifications.